have a look at this. class 1, condition 5 dictate the allowance of windows at or above ground floor level.
i assume you’re referring to skylights set into the roof, rather than on the side of the building. they wouldn’t really “face” into your neighbours garden as such, as in they wouldn’t invade their privacy. i’m assuming this from your description. a drawing would be useful.
i would suggest you contact the planning authority with a general enquiry to see where they stand on the issue. if the extension is exempt from PP, you could submit drawings and get a section 5, a certificate of exemption from the council, which would appease your neighbours if they object to the development, and also satisfy future purchasers that the extension is legal.